Jurors in Honolulu also found Naeem Williams guilty of the other four counts against him: aiding murder, conspiracy, obstruction of justice and making false statements.
Williams' lawyers had argued that while Williams beat his daughter Talia Williams, it's unclear whether he caused her July 2005 death.
The trial now moves to a penalty phase in which jurors will be asked to decide whether to sentence Williams to death. That phase starts Tuesday.
Hawaii doesn't have the death penalty because the state abolished capital punishment in 1957. But Williams is being tried in the federal system because the crime occurred on military property.
Williams and the girl's stepmother, Delilah Williams, have acknowledged beating, confining and restraining the child in the seven months before her death.
Delilah Williams made a deal with prosecutors in exchange for testimony against her husband. While on the witness stand, she testified she once stomped the girl until she felt bone crack.
Naeem Williams testified earlier this month that he beat daughter often because of her bathroom accidents and because he was taking out his marital frustrations on the child.
He told the jury of seven men and five women that the day Talia died, he had punched her repeatedly after a night of drinking. He hit her so hard in the back that she hit her head on the floor and appeared to have a seizure, he said.
Hawaii's history with capital punishment predates statehood. There have been 49 executions in Hawaii, the first in 1856 and the last recorded in 1944, according to the Death Penalty Information Center.
The last time the federal death penalty was approved for a Hawaii case was for a drug-related murder. But the defendant took a plea deal that gave him a life sentence, then died of an apparent suicide about three months later.
Sam Eifling can be reached on Twitter at http://twitter.com/seifling